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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...recombination between cDNA and a previous TE insertion.Adaptive evolution of TEsTransposable elements do not exclusively cause damage to the host. As sources of molecular variation, they can reroute regulation of gene expression (Trizzino et al. 2017; Sundaram and Wysocka 2020) and contribute to adaptive...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...are enriched in functions related to the regulation of immunity, such as interferon signaling and innate immune response (IRF2, IRF3, IRF5, IRF7, IRF9, IFI35, IFIT1, ISG20, IFNGR2, HLA-DQB1, CIITA, etc.), as well as proliferative (DNA repair, centrosome localization, etc.), housekeeping (ncRNA processing...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...and Goff 2009; Jacobs et al. 2014; Najafabadi et al. 2015; Schmitges et al. 2016; Imbeault et al. 2017; Bruno et al. 2019). TE-derived sequences make up a readily recognizable 50% of the human genomic DNA, a likely underestimation of their real contribution to our genetic makeup as their signature features...
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Dog Special/Letters: Short interspersed elements (SINEs) are a major source of canine genomic diversity
- Wei Wang and
- Ewen F. Kirkness
Genome Res. December 2005 15: 1798-1808; doi:10.1101/gr.3765505
...: In this window In a new window Figure 1. Construction of libraries that are enriched for SINEC_Cf elements and flanking sequence. ( A ) Genomic DNA is cleaved with the frequently cutting restriction enzyme, NlaIII. ( B ) The cleaved fragments are self-ligated. ( C ) The circularized products are subjected to PCR...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...S8), which correlated positively with gene density (chromosome scale rs = 0.84, P < 2.2 × 10−16) and negatively with DNA methylation (CG rs = −0.76, P < 2.2 × 10−16) and transposable element (TE) density (rs = −0.93, P < 2.2 × 10−16), as expected from previous work (Zhang et al. 2006, 2009...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...cell line and three technical replicates of its DNA methylation deficient variant DKO ( Rhee et al. 2002 ) were performed. The global unmethylation of each one of the genomic elements considered was estimated by analysis of the relative distribution of normalized reads ( nreads ) compared with number...
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LETTER: Human-specific insertions and deletions inferred from mammalian genome sequences
- Feng-Chi Chen,
- Chueng-Jong Chen,
- Wen-Hsiung Li,
- and Trees-Juen Chuang
Genome Res. January 2007 17: 16-22; Published in Advance November 9, 2006, doi:10.1101/gr.5429606
...of transposable elements mediated by short identical DNA segments in primates . Genome Res. 15 : 1243 – 1249 . ↵ Watanabe, H. , Fujiyama, A. , Hattori, M. , Taylor, T.D. , Toyoda, A. , Kuroki, Y. , Noguchi, H. , Ben, A. , Kahla, H. , Lehrach, R. , et al. ( 2004 ) DNA sequence and comparative analysis...
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Research: Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements
- Priscilla Turelli,
- Nathaly Castro-Diaz,
- Flavia Marzetta,
- Adamandia Kapopoulou,
- Charlène Raclot,
- Julien Duc,
- Vannary Tieng,
- Simon Quenneville,
- and Didier Trono
Genome Res. August 2014 24: 1260-1270; Published in Advance May 30, 2014, doi:10.1101/gr.172833.114
...repertoire via transposable elements. Genome Res 18: 1752–1762. Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E. 2006. At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. J Virol 80: 10752–10762. Cammas F...
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LETTER: Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
- Kateryna D. Makova,
- Shan Yang,
- and Francesca Chiaromonte
Genome Res. April 2004 14: 567-573; doi:10.1101/gr.1971104
...elements, and three families of DNA elements). The second set encompasses 0.3 Mb on chromosome X and 6.4 Mb on autosomes. Although we study the ARs inserted in the rodent–primate ancestor, only the branches from the rat–mouse common ancestor to rat and to mouse are analyzed. View this table: In this window...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...end-joining–based DNA double-strand repair (NHEJ) or microhomology-mediated break-induced replication (MMBIR); (3) mobile element (ME) insertion, and deletion events involving retrotransposons or DNA transposons; and (4) the shrinkage or expansion of a variable number of tandem repeats (VNTR) by DNA...

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